trim.pdbs: Filter or Trim a PDBs Object

In bio3d: Biological Structure Analysis

Filter or Trim a PDBs Object

Description

Trim residues and/or filter out structures from a PDBs object.

Usage

## S3 method for class 'pdbs'
trim(pdbs, row.inds=NULL, col.inds=NULL, ...)

Arguments

pdbs	an object of class pdbs as obtained from function pdbaln or read.fasta.pdb; a xyz matrix containing the cartesian coordinates of C-alpha atoms.
row.inds	a numeric vector of indices pointing to the PDB structures to keep (rows in the pdbs$ali matrix).
col.inds	a numeric vector of indices pointing to the alignment columns to keep (columns in the pdbs$ali matrix).
...	additional arguments passed to and from functions.

Details

Utility function to remove structures, or trim off columns, in a ‘pdbs’ object.

Value

Returns an updated ‘pdbs’ object with the following components:

xyz	numeric matrix of aligned C-alpha coordinates.
resno	character matrix of aligned residue numbers.
b	numeric matrix of aligned B-factor values.
chain	character matrix of aligned chain identifiers.
id	character vector of PDB sequence/structure names.
ali	character matrix of aligned sequences.
call	the matched call.

Author(s)

Lars Skjaerven

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

pdbaln, gap.inspect, read.fasta,read.fasta.pdb, trim.pdb,

Examples

## Not run: 
## Fetch PDB files and split to chain A only PDB files
ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
raw.files <- get.pdb(ids, path = "raw_pdbs")
files <- pdbsplit(raw.files, ids, path = "raw_pdbs/split_chain")

## Sequence Alignement, and connectivity check
pdbs <- pdbaln(files)

cons <- inspect.connectivity(pdbs)

## omit files with missing residues
trim.pdbs(pdbs, row.inds=which(cons))

## End(Not run)

bio3d documentation built on Oct. 27, 2022, 1:06 a.m.